Starting phenix.refine on Sat Dec 28 21:06:34 2024 by afonine =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_7718462.pdb Found miller_array, /net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz Found phil, /net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained_def.eff Processing PHIL parameters: ------------------------------------------------------------------------------- Adding PHIL files: ------------------ /net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained_def.eff No user-defined map coefficients or files defined; will use default map outputs instead. Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { phil_files = "/net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained_def.eff" default_phil = "/net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained_def.eff" model { file = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_7718462.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_7718462.pdb" miller_array { file = "/net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz" } default_miller_array = "/net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz" } refinement { electron_density_maps { map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT mtz_label_phases = PH2FOFCWT fill_missing_f_obs = True } map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT_no_fill mtz_label_phases = PH2FOFCWT_no_fill } map_coefficients { map_type = mFo-DFc mtz_label_amplitudes = FOFCWT mtz_label_phases = PHFOFCWT } map_coefficients { map_type = anomalous mtz_label_amplitudes = ANOM mtz_label_phases = PANOM } map { map_type = 2mFo-DFc fill_missing_f_obs = True } map { map_type = 2mFo-DFc } map { map_type = mFo-DFc } } refine { strategy = *individual_sites individual_sites_real_space rigid_body \ *individual_adp group_adp tls *occupancies group_anomalous \ den occupancies { individual = (chain A and resseq 15 and (name OE2 or name OE1)) or \ (chain A and resseq 24 and (name OD2 or name OD1)) } } main { ordered_solvent = True number_of_macro_cycles = 5 max_number_of_iterations = 100 } ordered_solvent { mode = second_half filter_only every_macro_cycle \ *every_macro_cycle_after_first primary_map_cutoff = 2.5 secondary_map_and_map_cc_filter { poor_map_value_threshold = 0.7 } ignore_final_filtering_step = True correct_drifted_waters = False } } Starting job =============================================================================== Symmetric amino acids flipped. Time to flip 2 residue(s): 0.00s Monomer Library directory: "/net/anaconda/raid1/afonine/phenix3/modules/chem_data/mon_lib" Total number of atoms: 3381 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3105 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 187, 2807 Classifications: {'peptide': 187} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 177} Conformer: "B" Number of residues, atoms: 187, 2807 Classifications: {'peptide': 187} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 177} bond proxies already assigned to first conformer: 2512 Chain: "A" Number of atoms: 276 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 254, 271 Unusual residues: {'DTT': 1} Classifications: {'undetermined': 1, 'water': 253} Link IDs: {None: 253} Conformer: "B" Number of residues, atoms: 253, 253 Classifications: {'water': 253} Link IDs: {None: 252} Residues with excluded nonbonded symmetry interactions: 32 residue: pdb=" N ALYS A 41 " occ=0.48 ... (42 atoms not shown) pdb=" HZ3BLYS A 41 " occ=0.52 residue: pdb=" N ACYS A 53 " occ=0.70 ... (20 atoms not shown) pdb=" HG BCYS A 53 " occ=0.30 residue: pdb=" N AGLU A 64 " occ=0.53 ... (28 atoms not shown) pdb=" HG3BGLU A 64 " occ=0.47 residue: pdb=" N AGLY A 65 " occ=0.53 ... (12 atoms not shown) pdb=" HA3BGLY A 65 " occ=0.47 residue: pdb=" N APRO A 66 " occ=0.53 ... (26 atoms not shown) pdb=" HD3BPRO A 66 " occ=0.47 residue: pdb=" N ATYR A 67 " occ=0.53 ... (40 atoms not shown) pdb=" HH BTYR A 67 " occ=0.47 residue: pdb=" N AASN A 76 " occ=0.75 ... (26 atoms not shown) pdb="HD22BASN A 76 " occ=0.25 residue: pdb=" N AGLN A 80 " occ=0.54 ... (32 atoms not shown) pdb="HE22BGLN A 80 " occ=0.46 residue: pdb=" N AGLU A 90 " occ=0.59 ... (28 atoms not shown) pdb=" HG3BGLU A 90 " occ=0.41 residue: pdb=" N ALYS A 93 " occ=0.57 ... (42 atoms not shown) pdb=" HZ3BLYS A 93 " occ=0.43 residue: pdb=" N AGLU A 94 " occ=0.48 ... (28 atoms not shown) pdb=" HG3BGLU A 94 " occ=0.52 residue: pdb=" N AGLU A 96 " occ=0.57 ... (28 atoms not shown) pdb=" HG3BGLU A 96 " occ=0.43 ... (remaining 20 not shown) Time building chain proxies: 2.31, per 1000 atoms: 0.68 Number of scatterers: 3381 At special positions: 0 Unit cell: (75.227, 75.227, 75.227, 90, 90, 120) Space group: P 31 2 1 (No. 152) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 10 16.00 O1- 2 9.00 O 551 8.00 N 265 7.00 C 957 6.00 H 1596 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.62 Conformation dependent library (CDL) restraints added in 279.5 milliseconds Time building geometry restraints manager: 0.79 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.64 - 0.91: 489 0.91 - 1.18: 1179 1.18 - 1.45: 695 1.45 - 1.72: 774 1.72 - 1.99: 16 Bond restraints: 3153 Sorted by residual: bond pdb=" CA ASP A 42 " pdb=" C ASP A 42 " ideal model delta sigma weight residual 1.528 1.310 0.218 1.11e-02 8.12e+03 3.86e+02 bond pdb=" CG HIS A 138 " pdb=" ND1 HIS A 138 " ideal model delta sigma weight residual 1.378 1.590 -0.212 1.10e-02 8.26e+03 3.72e+02 bond pdb=" CA GLU A 176 " pdb=" C GLU A 176 " ideal model delta sigma weight residual 1.524 1.766 -0.242 1.26e-02 6.30e+03 3.69e+02 bond pdb=" C ALA A 114 " pdb=" O ALA A 114 " ideal model delta sigma weight residual 1.237 1.009 0.228 1.19e-02 7.06e+03 3.66e+02 bond pdb=" N BLEU A 153 " pdb=" CA BLEU A 153 " ideal model delta sigma weight residual 1.458 1.677 -0.219 1.19e-02 7.06e+03 3.37e+02 ... (remaining 3148 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.70: 3153 4.70 - 9.40: 1878 9.40 - 14.10: 621 14.10 - 18.80: 117 18.80 - 23.50: 8 Bond angle restraints: 5777 Sorted by residual: angle pdb=" O GLY A 40 " pdb=" C GLY A 40 " pdb=" N BLYS A 41 " ideal model delta sigma weight residual 123.06 106.41 16.65 9.50e-01 1.11e+00 3.07e+02 angle pdb=" O LEU A 7 " pdb=" C LEU A 7 " pdb=" N VAL A 8 " ideal model delta sigma weight residual 123.27 140.11 -16.84 1.18e+00 7.18e-01 2.04e+02 angle pdb=" CA BASN A 76 " pdb=" C BASN A 76 " pdb=" O BASN A 76 " ideal model delta sigma weight residual 120.92 135.99 -15.07 1.12e+00 7.97e-01 1.81e+02 angle pdb=" CA GLY A 40 " pdb=" C GLY A 40 " pdb=" N BLYS A 41 " ideal model delta sigma weight residual 114.75 127.20 -12.45 9.90e-01 1.02e+00 1.58e+02 angle pdb=" O GLU A 16 " pdb=" C GLU A 16 " pdb=" N MET A 17 " ideal model delta sigma weight residual 122.12 135.42 -13.30 1.06e+00 8.90e-01 1.58e+02 ... (remaining 5772 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.76: 952 17.76 - 35.53: 114 35.53 - 53.29: 30 53.29 - 71.06: 13 71.06 - 88.82: 2 Dihedral angle restraints: 1111 sinusoidal: 852 harmonic: 259 Sorted by residual: dihedral pdb=" CA ASP A 49 " pdb=" C ASP A 49 " pdb=" N VAL A 50 " pdb=" CA VAL A 50 " ideal model delta harmonic sigma weight residual 180.00 151.81 28.19 0 5.00e+00 4.00e-02 3.18e+01 dihedral pdb=" CA ARG A 156 " pdb=" C ARG A 156 " pdb=" N GLY A 157 " pdb=" CA GLY A 157 " ideal model delta harmonic sigma weight residual 180.00 -156.61 -23.39 0 5.00e+00 4.00e-02 2.19e+01 dihedral pdb=" ND1 HIS A 126 " pdb=" CG HIS A 126 " pdb=" CD2 HIS A 126 " pdb=" HD2 HIS A 126 " ideal model delta harmonic sigma weight residual 180.00 158.36 21.64 0 5.00e+00 4.00e-02 1.87e+01 ... (remaining 1108 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.224: 107 0.224 - 0.447: 82 0.447 - 0.671: 34 0.671 - 0.894: 17 0.894 - 1.117: 3 Chirality restraints: 243 Sorted by residual: chirality pdb=" CG LEU A 172 " pdb=" CB LEU A 172 " pdb=" CD1 LEU A 172 " pdb=" CD2 LEU A 172 " both_signs ideal model delta sigma weight residual False -2.59 -1.47 -1.12 2.00e-01 2.50e+01 3.12e+01 chirality pdb=" CB VAL A 69 " pdb=" CA VAL A 69 " pdb=" CG1 VAL A 69 " pdb=" CG2 VAL A 69 " both_signs ideal model delta sigma weight residual False -2.63 -1.55 -1.08 2.00e-01 2.50e+01 2.91e+01 chirality pdb=" CB VAL A 181 " pdb=" CA VAL A 181 " pdb=" CG1 VAL A 181 " pdb=" CG2 VAL A 181 " both_signs ideal model delta sigma weight residual False -2.63 -3.56 0.93 2.00e-01 2.50e+01 2.17e+01 ... (remaining 240 not shown) Planarity restraints: 488 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 119 " 0.010 2.00e-02 2.50e+03 6.55e-02 1.29e+02 pdb=" CG PHE A 119 " -0.092 2.00e-02 2.50e+03 pdb=" CD1 PHE A 119 " -0.046 2.00e-02 2.50e+03 pdb=" CD2 PHE A 119 " 0.103 2.00e-02 2.50e+03 pdb=" CE1 PHE A 119 " -0.004 2.00e-02 2.50e+03 pdb=" CE2 PHE A 119 " -0.026 2.00e-02 2.50e+03 pdb=" CZ PHE A 119 " 0.047 2.00e-02 2.50e+03 pdb=" HD1 PHE A 119 " 0.123 2.00e-02 2.50e+03 pdb=" HD2 PHE A 119 " -0.066 2.00e-02 2.50e+03 pdb=" HE1 PHE A 119 " -0.083 2.00e-02 2.50e+03 pdb=" HE2 PHE A 119 " 0.030 2.00e-02 2.50e+03 pdb=" HZ PHE A 119 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS A 138 " 0.090 2.00e-02 2.50e+03 6.71e-02 1.01e+02 pdb=" CG HIS A 138 " -0.066 2.00e-02 2.50e+03 pdb=" ND1 HIS A 138 " -0.017 2.00e-02 2.50e+03 pdb=" CD2 HIS A 138 " 0.031 2.00e-02 2.50e+03 pdb=" CE1 HIS A 138 " 0.016 2.00e-02 2.50e+03 pdb=" NE2 HIS A 138 " -0.084 2.00e-02 2.50e+03 pdb=" HD1 HIS A 138 " -0.083 2.00e-02 2.50e+03 pdb=" HD2 HIS A 138 " 0.002 2.00e-02 2.50e+03 pdb=" HE1 HIS A 138 " 0.112 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS A 126 " 0.024 2.00e-02 2.50e+03 6.36e-02 9.10e+01 pdb=" CG HIS A 126 " -0.111 2.00e-02 2.50e+03 pdb=" ND1 HIS A 126 " 0.063 2.00e-02 2.50e+03 pdb=" CD2 HIS A 126 " -0.071 2.00e-02 2.50e+03 pdb=" CE1 HIS A 126 " 0.039 2.00e-02 2.50e+03 pdb=" NE2 HIS A 126 " -0.050 2.00e-02 2.50e+03 pdb=" HD2 HIS A 126 " 0.103 2.00e-02 2.50e+03 pdb=" HE1 HIS A 126 " 0.002 2.00e-02 2.50e+03 pdb=" HE2 HIS A 126 " -0.001 2.00e-02 2.50e+03 ... (remaining 485 not shown) Histogram of nonbonded interaction distances: 1.78 - 2.35: 1226 2.35 - 2.91: 8308 2.91 - 3.47: 10369 3.47 - 4.04: 15199 4.04 - 4.60: 21558 Nonbonded interactions: 56660 Sorted by model distance: nonbonded pdb=" H GLY A 157 " pdb=" HG1 THR A 160 " model vdw 1.784 2.100 nonbonded pdb=" HG SER A 47 " pdb="HH11 ARG A 48 " model vdw 1.791 2.100 nonbonded pdb=" H GLY A 159 " pdb=" O LEU A 185 " model vdw sym.op. 1.816 2.450 x-y,-y,-z-4/3 nonbonded pdb=" O GLU A 147 " pdb=" H BTHR A 154 " model vdw 1.827 2.450 nonbonded pdb=" HG SER A 155 " pdb=" H ARG A 156 " model vdw 1.832 2.100 ... (remaining 56655 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. ============================== Scattering factors ============================= ----------X-ray scattering dictionary---------- Number of scattering types: 6 Type Number sf(0) Gaussians S 10 15.96 2 O1- 2 8.97 3 O 551 7.97 2 N 265 6.97 2 C 957 5.97 2 H 1596 1.00 2 sf(0) = scattering factor at diffraction angle 0. =========================== Regularize ADP if needed ========================== ========================== Anomalous scatterer groups ========================= All atoms refined with f_prime=0 and f_double_prime=0. ====================== Modifying start model if requested ===================== ******************************************************************************* Automatic adjustment: hydrogens.refine=riding ******************************************************************************* n_use = 3381 n_use_u_iso = 1596 n_use_u_aniso = 1785 n_grad_site = 0 n_grad_u_iso = 0 n_grad_u_aniso = 0 n_grad_occupancy = 0 n_grad_fp = 0 n_grad_fdp = 0 total number of scatterers = 3381 ================== Extract refinement strategy and selections ================= Refinement flags and selection counts: individual_sites = True (3381 atoms) torsion_angles = False (0 atoms) rigid_body = False (0 atoms in 0 groups) individual_adp = True (iso = 1596 aniso = 1785) group_adp = False (0 atoms in 0 groups) tls = False (0 atoms in 0 groups) occupancies = True (876 atoms) group_anomalous = False ============================ Non-default parameters =========================== A complete record of all parameters was written to the .eff file above. Below are only the non-defaults. #phil __ON__ refinement { electron_density_maps { map_coefficients { map_type = "2mFo-DFc" mtz_label_amplitudes = "2FOFCWT" mtz_label_phases = "PH2FOFCWT" fill_missing_f_obs = True } map_coefficients { map_type = "2mFo-DFc" mtz_label_amplitudes = "2FOFCWT_no_fill" mtz_label_phases = "PH2FOFCWT_no_fill" } map_coefficients { map_type = "mFo-DFc" mtz_label_amplitudes = "FOFCWT" mtz_label_phases = "PHFOFCWT" } map_coefficients { map_type = "anomalous" mtz_label_amplitudes = "ANOM" mtz_label_phases = "PANOM" } map { map_type = "2mFo-DFc" fill_missing_f_obs = True } map { map_type = "2mFo-DFc" } map { map_type = "mFo-DFc" } } refine { strategy = *individual_sites individual_sites_real_space rigid_body \ *individual_adp group_adp tls *occupancies group_anomalous den occupancies { individual = (chain A and resseq 15 and (name OE2 or name OE1)) or \ (chain A and resseq 24 and (name OD2 or name OD1)) } } main { ordered_solvent = True number_of_macro_cycles = 5 max_number_of_iterations = 100 } hydrogens { refine = individual *riding Auto } pdb_interpretation { c_beta_restraints = False } ordered_solvent { mode = second_half filter_only every_macro_cycle \ *every_macro_cycle_after_first primary_map_cutoff = 2.5 secondary_map_and_map_cc_filter { poor_map_value_threshold = 0.7 } ignore_final_filtering_step = True correct_drifted_waters = False } } output { prefix = "shake_7718462_refine" serial = 1 target_output_format = None *pdb mmcif } #phil __OFF__ ================================== Hydrogens ================================== Total: count: 1596 occupancy sum: 1438.50 (% of total atoms 46.85) Rotatable: count: 507 occupancy sum: 483.00 (% of total atoms 15.73) ----------structure factors based statistics (before refinement)---------- ----------X-ray data---------- |--(resolution: 1.15 - 49.25 A, n_refl.=87602 (all), 4.90 % free)------------| | | | r_work= 0.2606 r_free= 0.1944 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 2.791261 | | target function (ml) not normalized (work): 232528.758867 | | target function (ml) not normalized (free): 11808.326958 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 49.25 - 3.58 1.00 2941 171 0.3035 0.2158 6.988 4.9563| | 2: 3.57 - 2.84 1.00 2876 122 0.2453 0.1779 4.3605 4.3436| | 3: 2.84 - 2.48 1.00 2833 165 0.2321 0.1689 4.138 4.1809| | 4: 2.47 - 2.25 1.00 2825 136 0.2337 0.1330 3.844 3.8279| | 5: 2.25 - 2.09 1.00 2756 127 0.2483 0.1605 3.8063 3.8349| | 6: 2.09 - 1.97 1.00 2846 113 0.2531 0.1782 3.4719 3.4987| | 7: 1.97 - 1.87 1.00 2787 165 0.2509 0.1762 3.1401 3.2056| | 8: 1.87 - 1.79 1.00 2789 144 0.2412 0.1878 3.0447 3.1174| | 9: 1.79 - 1.72 1.00 2745 138 0.2461 0.1968 2.9058 2.9837| | 10: 1.72 - 1.66 1.00 2789 158 0.2428 0.1891 2.7991 2.8369| | 11: 1.66 - 1.61 1.00 2740 147 0.2472 0.1620 2.7412 2.6834| | 12: 1.61 - 1.56 1.00 2787 146 0.2509 0.2053 2.6355 2.6229| | 13: 1.56 - 1.52 1.00 2745 130 0.2573 0.1823 2.5767 2.5933| | 14: 1.52 - 1.48 1.00 2803 134 0.2639 0.1772 2.5103 2.4709| | 15: 1.48 - 1.45 1.00 2738 128 0.2608 0.2208 2.4341 2.5274| | 16: 1.45 - 1.42 1.00 2756 161 0.2642 0.2059 2.3973 2.4163| | 17: 1.42 - 1.39 1.00 2785 139 0.2651 0.1918 2.3309 2.293| | 18: 1.39 - 1.36 1.00 2741 179 0.2701 0.2263 2.2792 2.3686| | 19: 1.36 - 1.34 1.00 2807 134 0.2677 0.2295 2.2449 2.2671| | 20: 1.34 - 1.32 1.00 2696 147 0.2658 0.2184 2.1849 2.2147| | 21: 1.32 - 1.30 1.00 2785 112 0.2717 0.2313 2.1495 2.2005| | 22: 1.29 - 1.27 1.00 2704 152 0.2753 0.2690 2.1314 2.2395| | 23: 1.27 - 1.26 1.00 2802 156 0.2773 0.2486 2.109 2.1772| | 24: 1.26 - 1.24 1.00 2744 132 0.2769 0.2241 2.0745 2.0929| | 25: 1.24 - 1.22 1.00 2734 148 0.2884 0.2586 2.0619 2.0798| | 26: 1.22 - 1.21 1.00 2727 135 0.2904 0.2409 2.0267 2.0756| | 27: 1.21 - 1.19 1.00 2814 148 0.2984 0.3013 2.0121 2.065| | 28: 1.19 - 1.18 1.00 2671 147 0.2990 0.3103 1.9887 2.0582| | 29: 1.18 - 1.16 1.00 2800 134 0.2934 0.2822 1.9649 2.053| | 30: 1.16 - 1.15 1.00 2740 148 0.3002 0.2990 1.9334 1.9998| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |R-free likelihood based estimates for figures of merit, absolute phase error,| |and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)| | | | Bin Resolution No. Refl. FOM Phase Scale Alpha Beta | | # range work test error factor | | 1: 49.25 - 3.58 2941 171 0.87 19.06 0.76 0.23 1523.04| | 2: 3.57 - 2.84 2876 122 0.80 26.39 1.27 0.23 1523.04| | 3: 2.84 - 2.48 2833 165 0.74 32.30 1.24 0.23 1262.65| | 4: 2.47 - 2.25 2825 136 0.81 25.81 1.25 0.25 586.88| | 5: 2.25 - 2.09 2756 127 0.77 29.65 1.28 0.25 586.88| | 6: 2.09 - 1.97 2846 113 0.83 22.99 1.29 0.25 320.02| | 7: 1.97 - 1.87 2787 165 0.90 16.61 1.28 0.26 92.43| | 8: 1.87 - 1.79 2789 144 0.86 21.29 1.25 0.26 92.43| | 9: 1.79 - 1.72 2745 138 0.88 18.31 1.24 0.26 54.77| | 10: 1.72 - 1.66 2789 158 0.87 20.01 1.23 0.26 47.23| | 11: 1.66 - 1.61 2740 147 0.86 21.01 1.24 0.26 45.48| | 12: 1.61 - 1.56 2787 146 0.89 17.74 1.23 0.25 27.71| | 13: 1.56 - 1.52 2745 130 0.87 19.49 1.24 0.25 27.71| | 14: 1.52 - 1.48 2803 134 0.87 20.25 1.24 0.25 24.79| | 15: 1.48 - 1.45 2738 128 0.88 19.18 1.23 0.25 19.44| | 16: 1.45 - 1.42 2756 161 0.87 20.51 1.23 0.25 19.44| | 17: 1.42 - 1.39 2785 139 0.87 20.11 1.23 0.25 16.84| | 18: 1.39 - 1.36 2741 179 0.87 20.62 1.23 0.25 15.33| | 19: 1.36 - 1.34 2807 134 0.86 21.53 1.23 0.25 15.33| | 20: 1.34 - 1.32 2696 147 0.87 20.74 1.21 0.25 12.99| | 21: 1.32 - 1.30 2785 112 0.86 22.03 1.21 0.25 12.82| | 22: 1.29 - 1.27 2704 152 0.85 22.40 1.22 0.25 12.58| | 23: 1.27 - 1.26 2802 156 0.85 22.36 1.21 0.24 11.32| | 24: 1.26 - 1.24 2744 132 0.85 22.93 1.21 0.24 11.32| | 25: 1.24 - 1.22 2734 148 0.84 24.14 1.21 0.24 10.97| | 26: 1.22 - 1.21 2727 135 0.83 24.73 1.21 0.23 10.59| | 27: 1.21 - 1.19 2814 148 0.82 25.77 1.20 0.23 10.59| | 28: 1.19 - 1.18 2671 147 0.80 27.30 1.18 0.22 10.41| | 29: 1.18 - 1.16 2800 134 0.80 27.75 1.17 0.22 10.35| | 30: 1.16 - 1.15 2740 148 0.78 29.30 1.15 0.22 10.35| |alpha: min = 0.22 max = 0.26 mean = 0.24| |beta: min = 10.35 max = 1523.04 mean = 220.24| |figures of merit: min = 0.00 max = 1.00 mean = 0.84| |phase err.(work): min = 0.00 max = 89.99 mean = 22.74| |phase err.(test): min = 0.00 max = 89.75 mean = 22.89| |-----------------------------------------------------------------------------| ----------Initial model statistics (before refinement)---------- Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.084 0.258 1557 Z= 5.613 Angle : 5.190 17.692 2118 Z= 3.674 Chirality : 0.371 1.117 243 Planarity : 0.029 0.127 284 Dihedral : 13.817 88.820 611 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 1.86 % Allowed : 3.11 % Favored : 95.03 % Cbeta Deviations : 28.65 % Peptide Plane: Cis-proline : 18.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.78 (0.49), residues: 224 helix: -2.06 (0.41), residues: 102 sheet: -1.01 (0.66), residues: 40 loop : 0.38 (0.65), residues: 82 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.052 0.012 ARG A 98 TYR 0.073 0.030 TYR A 141 PHE 0.097 0.045 PHE A 162 HIS 0.061 0.030 HIS A 138 Individual atomic B min max mean iso aniso Overall: 8.85 119.30 19.89 3.90 0 1785 Protein: 8.85 115.78 16.79 3.90 0 1519 Water: 11.36 119.30 38.03 N/A 0 258 Other: 19.04 26.29 21.71 N/A 0 8 Chain A: 8.85 119.30 19.89 N/A 0 1785 Histogram: Values Number of atoms 8.85 - 19.89 1276 19.89 - 30.94 224 30.94 - 41.98 127 41.98 - 53.03 89 53.03 - 64.07 44 64.07 - 75.12 11 75.12 - 86.16 7 86.16 - 97.21 4 97.21 - 108.25 1 108.25 - 119.30 2 |-Occupancies statistics------------------------------------------------------| | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1 = 0 | |-----------------------------------------------------------------------------| =================== Write initial parameters into .eff file =================== *********************** REFINEMENT MACRO_CYCLE 1 OF 5 ************************* |--(resolution: 1.15 - 49.25 A, n_refl.=87602 (all), 4.90 % free)------------| | | | r_work= 0.2606 r_free= 0.1944 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 2.791261 | | target function (ml) not normalized (work): 232528.758867 | | target function (ml) not normalized (free): 11808.326958 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2566 0.2607 0.1944 n_refl.: 87602 re-set all scales: r(all,work,free)=0.2566 0.2607 0.1944 n_refl.: 87602 remove outliers: r(all,work,free)=0.1982 0.1986 0.1944 n_refl.: 87594 overall B=0.19 to atoms: r(all,work,free)=0.2004 0.2009 0.1956 n_refl.: 87594 bulk-solvent and scaling: r(all,work,free)=0.1644 0.1637 0.1783 n_refl.: 87594 remove outliers: r(all,work,free)=0.1644 0.1636 0.1783 n_refl.: 87593 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 98.94 88 5 0.3823 386.712 359.539 0.680 1.003 0.415 11.894-9.307 99.02 97 4 0.1797 614.272 595.813 0.933 1.003 0.404 9.237-7.194 100.00 213 7 0.2094 502.399 493.521 0.955 1.004 0.344 7.162-5.571 100.00 427 22 0.2170 377.023 366.114 0.935 1.004 0.330 5.546-4.326 100.00 867 58 0.1290 517.559 511.789 0.962 1.004 0.219 4.315-3.360 100.00 1859 96 0.1147 492.202 487.995 1.006 1.003 0.199 3.356-2.611 100.00 3867 181 0.1445 323.351 320.284 0.998 1.003 0.090 2.608-2.026 99.99 8198 413 0.1350 214.352 212.384 1.007 1.001 0.000 2.025-1.573 100.00 17313 902 0.1638 104.679 103.981 1.011 0.999 0.000 1.573-1.221 100.00 36679 1900 0.2075 46.419 45.096 1.005 0.996 0.000 1.221-1.150 99.97 13689 708 0.2581 29.247 27.055 0.977 0.993 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0016 b_overall=0.0425 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1636 r_free=0.1783 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 76 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 r_work=0.1636 r_free=0.1783 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 26.773850 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 2034.187299 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1210 0.1465 0.0255 0.008 1.0 1.0 0.5 0.0 0 13.387 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.10 14.65 2.55 3.013 19.044 2034.187 0.017 12.39 15.41 3.01 3.205 19.539 2034.187 0.016 Individual atomic B min max mean iso aniso Overall: 8.55 118.78 21.01 2.87 0 1785 Protein: 8.55 118.78 17.89 2.87 0 1519 Water: 11.03 114.48 39.12 N/A 0 258 Other: 22.79 36.40 29.09 N/A 0 8 Chain A: 8.55 118.78 21.01 N/A 0 1785 Histogram: Values Number of atoms 8.55 - 19.58 1207 19.58 - 30.60 230 30.60 - 41.62 165 41.62 - 52.65 100 52.65 - 63.67 54 63.67 - 74.69 16 74.69 - 85.72 6 85.72 - 96.74 4 96.74 - 107.76 0 107.76 - 118.78 3 =========================== Idealize ADP of riding H ========================== r_work=0.1240 r_free=0.1541 r_work=0.1245 r_free=0.1546 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1245 r_free = 0.1546 target_work(ls_wunit_k1) = 0.016 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1244 r_free = 0.1547 target_work(ls_wunit_k1) = 0.015 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 2 OF 5 ************************* |--(resolution: 1.15 - 32.57 A, n_refl.=87593 (all), 4.90 % free)------------| | | | r_work= 0.1244 r_free= 0.1547 coordinate error (max.-lik. estimate): 0.10 A | | | | normalized target function (ls_wunit_k1) (work): 0.015431 | | target function (ls_wunit_k1) not normalized (work): 1285.335042 | | target function (ls_wunit_k1) not normalized (free): 114.873895 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1258 0.1244 0.1547 n_refl.: 87593 re-set all scales: r(all,work,free)=0.1700 0.1699 0.1766 n_refl.: 87593 remove outliers: r(all,work,free)=0.1700 0.1699 0.1766 n_refl.: 87593 overall B=0.13 to atoms: r(all,work,free)=0.1722 0.1721 0.1781 n_refl.: 87593 bulk-solvent and scaling: r(all,work,free)=0.1255 0.1241 0.1538 n_refl.: 87593 remove outliers: r(all,work,free)=0.1255 0.1241 0.1538 n_refl.: 87592 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 95.83 87 5 0.3615 299.147 278.279 0.637 1.002 0.380 11.894-9.307 99.02 97 4 0.1609 479.216 466.731 0.908 1.003 0.380 9.237-7.194 100.00 213 7 0.1816 391.940 386.703 0.948 1.003 0.340 7.162-5.571 100.00 427 22 0.1746 294.129 288.480 0.924 1.003 0.290 5.546-4.326 100.00 867 58 0.0924 403.767 401.025 0.950 1.003 0.204 4.315-3.360 100.00 1859 96 0.0776 383.985 383.048 0.995 1.003 0.190 3.356-2.611 100.00 3867 181 0.1018 252.258 251.580 0.999 1.002 0.110 2.608-2.026 99.99 8198 413 0.0973 167.224 166.649 1.010 1.002 0.000 2.025-1.573 100.00 17313 902 0.1207 81.664 81.861 1.017 1.000 0.000 1.573-1.221 100.00 36679 1900 0.1645 36.213 35.675 1.006 0.998 0.000 1.221-1.150 99.97 13689 708 0.2358 22.817 21.332 0.969 0.997 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0047 b_overall=0.0518 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1241 r_free=0.1538 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 GLN ** A 76 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 r_work=0.1242 r_free=0.1540 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1242 r_free=0.1540 | n_water=258 | time (s): 2.490 (total time: 2.490) Filter (dist) r_work=0.1251 r_free=0.1536 | n_water=252 | time (s): 25.810 (total time: 28.300) Filter (q & B) r_work=0.1255 r_free=0.1536 | n_water=249 | time (s): 3.880 (total time: 32.180) Compute maps r_work=0.1255 r_free=0.1536 | n_water=249 | time (s): 1.960 (total time: 34.140) Filter (map) r_work=0.1265 r_free=0.1543 | n_water=237 | time (s): 4.010 (total time: 38.150) Find peaks r_work=0.1265 r_free=0.1543 | n_water=237 | time (s): 0.760 (total time: 38.910) Add new water r_work=0.1423 r_free=0.1705 | n_water=453 | time (s): 3.800 (total time: 42.710) Refine new water occ: r_work=0.1335 r_free=0.1562 adp: r_work=0.1253 r_free=0.1512 occ: r_work=0.1269 r_free=0.1504 adp: r_work=0.1231 r_free=0.1491 occ: r_work=0.1235 r_free=0.1475 adp: r_work=0.1225 r_free=0.1475 ADP+occupancy (water only), MIN, final r_work=0.1225 r_free=0.1475 r_work=0.1225 r_free=0.1475 | n_water=453 | time (s): 111.730 (total time: 154.440) Filter (q & B) r_work=0.1232 r_free=0.1478 | n_water=429 | time (s): 3.860 (total time: 158.300) Filter (dist only) r_work=0.1232 r_free=0.1478 | n_water=429 | time (s): 40.060 (total time: 198.360) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 24.869089 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 1498.032599 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1227 0.1505 0.0278 0.007 0.9 1.9 0.5 0.0 0 12.435 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.27 15.05 2.78 3.789 23.203 1498.033 0.015 12.02 14.73 2.71 4.291 23.012 1498.033 0.015 Individual atomic B min max mean iso aniso Overall: 8.77 113.92 23.19 2.62 192 1764 Protein: 8.77 113.92 17.61 2.62 0 1519 Water: 10.97 79.80 42.82 N/A 192 237 Other: 25.72 36.11 30.41 N/A 0 8 Chain A: 8.77 113.92 20.36 N/A 0 1764 Chain S: 15.88 79.80 49.17 N/A 192 0 Histogram: Values Number of atoms 8.77 - 19.29 1210 19.29 - 29.80 244 29.80 - 40.32 186 40.32 - 50.83 140 50.83 - 61.35 114 61.35 - 71.86 48 71.86 - 82.37 8 82.37 - 92.89 3 92.89 - 103.40 1 103.40 - 113.92 2 =========================== Idealize ADP of riding H ========================== r_work=0.1202 r_free=0.1473 r_work=0.1202 r_free=0.1472 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1202 r_free = 0.1472 target_work(ls_wunit_k1) = 0.015 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1203 r_free = 0.1468 target_work(ls_wunit_k1) = 0.014 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 3 OF 5 ************************* |--(resolution: 1.15 - 32.57 A, n_refl.=87592 (all), 4.90 % free)------------| | | | r_work= 0.1203 r_free= 0.1468 coordinate error (max.-lik. estimate): 0.10 A | | | | normalized target function (ls_wunit_k1) (work): 0.014199 | | target function (ls_wunit_k1) not normalized (work): 1182.683420 | | target function (ls_wunit_k1) not normalized (free): 100.075411 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1216 0.1203 0.1468 n_refl.: 87592 re-set all scales: r(all,work,free)=0.1609 0.1606 0.1694 n_refl.: 87592 remove outliers: r(all,work,free)=0.1609 0.1606 0.1694 n_refl.: 87592 overall B=0.04 to atoms: r(all,work,free)=0.1615 0.1612 0.1698 n_refl.: 87592 bulk-solvent and scaling: r(all,work,free)=0.1213 0.1200 0.1466 n_refl.: 87592 remove outliers: r(all,work,free)=0.1211 0.1198 0.1466 n_refl.: 87588 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 91.67 83 5 0.3433 291.839 271.141 0.591 1.002 0.364 11.894-9.307 99.02 97 4 0.1501 479.216 477.178 0.921 1.003 0.360 9.237-7.194 100.00 213 7 0.1700 391.940 392.669 0.979 1.003 0.280 7.162-5.571 100.00 427 22 0.1506 294.129 291.218 0.938 1.003 0.256 5.546-4.326 100.00 867 58 0.0854 403.767 400.675 0.957 1.003 0.217 4.315-3.360 100.00 1859 96 0.0717 383.985 383.128 1.002 1.002 0.215 3.356-2.611 100.00 3867 181 0.0962 252.258 251.428 1.008 1.002 0.150 2.608-2.026 99.99 8198 413 0.0961 167.224 166.739 1.018 1.001 0.000 2.025-1.573 100.00 17313 902 0.1178 81.664 81.872 1.027 1.000 0.000 1.573-1.221 100.00 36679 1900 0.1609 36.213 35.710 1.016 0.998 0.000 1.221-1.150 99.97 13689 708 0.2332 22.817 21.350 0.976 0.996 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0151 b_overall=0.0619 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1198 r_free=0.1466 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 76 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 r_work=0.1198 r_free=0.1466 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1198 r_free=0.1466 | n_water=429 | time (s): 2.200 (total time: 2.200) Filter (dist) r_work=0.1200 r_free=0.1464 | n_water=426 | time (s): 39.460 (total time: 41.660) Filter (q & B) r_work=0.1201 r_free=0.1466 | n_water=425 | time (s): 3.550 (total time: 45.210) Compute maps r_work=0.1201 r_free=0.1466 | n_water=425 | time (s): 1.650 (total time: 46.860) Filter (map) r_work=0.1237 r_free=0.1466 | n_water=294 | time (s): 3.410 (total time: 50.270) Find peaks r_work=0.1237 r_free=0.1466 | n_water=294 | time (s): 0.710 (total time: 50.980) Add new water r_work=0.1362 r_free=0.1605 | n_water=481 | time (s): 2.600 (total time: 53.580) Refine new water occ: r_work=0.1265 r_free=0.1529 adp: r_work=0.1266 r_free=0.1530 occ: r_work=0.1243 r_free=0.1503 adp: r_work=0.1241 r_free=0.1505 occ: r_work=0.1228 r_free=0.1485 adp: r_work=0.1221 r_free=0.1484 ADP+occupancy (water only), MIN, final r_work=0.1221 r_free=0.1484 r_work=0.1221 r_free=0.1484 | n_water=481 | time (s): 165.400 (total time: 218.980) Filter (q & B) r_work=0.1226 r_free=0.1482 | n_water=448 | time (s): 2.630 (total time: 221.610) Filter (dist only) r_work=0.1226 r_free=0.1482 | n_water=448 | time (s): 34.700 (total time: 256.310) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 2.011559 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 41.653351 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1229 0.1453 0.0224 0.006 0.9 1.6 0.5 0.0 0 1.006 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.29 14.53 2.24 3.616 22.136 41.653 3.726 12.24 14.17 1.92 4.055 21.954 41.653 3.662 Individual atomic B min max mean iso aniso Overall: 9.19 109.55 21.80 2.28 213 1762 Protein: 9.19 109.55 17.22 2.28 0 1519 Water: 11.49 72.02 37.21 N/A 213 235 Other: 21.54 32.38 27.49 N/A 0 8 Chain A: 9.19 109.55 19.94 N/A 0 1762 Chain S: 15.69 72.02 37.16 N/A 213 0 Histogram: Values Number of atoms 9.19 - 19.23 1238 19.23 - 29.26 267 29.26 - 39.30 215 39.30 - 49.34 136 49.34 - 59.37 84 59.37 - 69.41 20 69.41 - 79.45 9 79.45 - 89.48 3 89.48 - 99.52 1 99.52 - 109.55 2 =========================== Idealize ADP of riding H ========================== r_work=0.1224 r_free=0.1417 r_work=0.1226 r_free=0.1418 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1226 r_free = 0.1418 target_work(ml) = 3.662 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1220 r_free = 0.1417 target_work(ml) = 3.659 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 4 OF 5 ************************* |--(resolution: 1.15 - 32.57 A, n_refl.=87588 (all), 4.90 % free)------------| | | | r_work= 0.1220 r_free= 0.1417 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.659226 | | target function (ml) not normalized (work): 304784.247491 | | target function (ml) not normalized (free): 16086.706223 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1229 0.1220 0.1417 n_refl.: 87588 re-set all scales: r(all,work,free)=0.1548 0.1547 0.1583 n_refl.: 87588 remove outliers: r(all,work,free)=0.1548 0.1547 0.1583 n_refl.: 87588 overall B=-0.01 to atoms: r(all,work,free)=0.1546 0.1545 0.1582 n_refl.: 87588 bulk-solvent and scaling: r(all,work,free)=0.1219 0.1211 0.1379 n_refl.: 87588 remove outliers: r(all,work,free)=0.1214 0.1206 0.1379 n_refl.: 87577 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 88.54 80 5 0.3798 283.763 259.931 0.463 0.999 0.295 11.894-9.307 96.08 94 4 0.2328 468.916 458.467 0.850 1.001 0.277 9.237-7.194 97.73 208 7 0.2336 384.554 384.640 0.947 1.002 0.204 7.162-5.571 100.00 427 22 0.2077 294.129 284.169 0.911 1.002 0.177 5.546-4.326 100.00 867 58 0.1112 403.767 399.403 0.952 1.002 0.170 4.315-3.360 100.00 1859 96 0.0936 383.985 381.487 0.993 1.002 0.170 3.356-2.611 100.00 3867 181 0.1167 252.258 249.958 0.999 1.002 0.150 2.608-2.026 99.99 8198 413 0.1054 167.224 166.208 1.012 1.001 0.000 2.025-1.573 100.00 17313 902 0.1025 81.664 81.785 1.026 1.000 0.000 1.573-1.221 100.00 36679 1900 0.1302 36.213 35.777 1.018 0.999 0.000 1.221-1.150 99.97 13689 708 0.2137 22.817 21.418 0.976 0.998 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0049 b_overall=-0.0237 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1206 r_free=0.1379 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 ASN A Total number of N/Q/H flips: 1 r_work=0.1206 r_free=0.1382 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1206 r_free=0.1382 | n_water=448 | time (s): 1.620 (total time: 1.620) Filter (dist) r_work=0.1206 r_free=0.1382 | n_water=448 | time (s): 35.580 (total time: 37.200) Filter (q & B) r_work=0.1206 r_free=0.1381 | n_water=447 | time (s): 3.040 (total time: 40.240) Compute maps r_work=0.1206 r_free=0.1381 | n_water=447 | time (s): 1.330 (total time: 41.570) Filter (map) r_work=0.1225 r_free=0.1384 | n_water=313 | time (s): 3.020 (total time: 44.590) Find peaks r_work=0.1225 r_free=0.1384 | n_water=313 | time (s): 0.500 (total time: 45.090) Add new water r_work=0.1301 r_free=0.1432 | n_water=486 | time (s): 3.310 (total time: 48.400) Refine new water occ: r_work=0.1225 r_free=0.1381 adp: r_work=0.1225 r_free=0.1383 occ: r_work=0.1210 r_free=0.1374 adp: r_work=0.1207 r_free=0.1373 occ: r_work=0.1200 r_free=0.1374 adp: r_work=0.1195 r_free=0.1372 ADP+occupancy (water only), MIN, final r_work=0.1195 r_free=0.1372 r_work=0.1195 r_free=0.1372 | n_water=486 | time (s): 276.430 (total time: 324.830) Filter (q & B) r_work=0.1202 r_free=0.1373 | n_water=445 | time (s): 3.350 (total time: 328.180) Filter (dist only) r_work=0.1202 r_free=0.1373 | n_water=445 | time (s): 33.620 (total time: 361.800) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.882976 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 48.442858 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1205 0.1371 0.0166 0.006 0.9 1.9 0.5 0.0 0 0.941 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.05 13.71 1.66 3.414 21.563 48.443 3.643 11.86 13.57 1.70 3.966 21.384 48.443 3.624 Individual atomic B min max mean iso aniso Overall: 9.25 105.99 21.26 2.18 211 1761 Protein: 9.25 105.99 16.81 2.18 0 1519 Water: 11.44 70.05 36.37 N/A 211 234 Other: 21.17 30.11 25.51 N/A 0 8 Chain A: 9.25 105.99 19.47 N/A 0 1761 Chain S: 16.11 70.05 36.20 N/A 211 0 Histogram: Values Number of atoms 9.25 - 18.92 1237 18.92 - 28.60 279 28.60 - 38.27 209 38.27 - 47.94 132 47.94 - 57.62 74 57.62 - 67.29 28 67.29 - 76.97 8 76.97 - 86.64 2 86.64 - 96.31 1 96.31 - 105.99 2 =========================== Idealize ADP of riding H ========================== r_work=0.1186 r_free=0.1357 r_work=0.1187 r_free=0.1357 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1187 r_free = 0.1357 target_work(ml) = 3.624 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1181 r_free = 0.1354 target_work(ml) = 3.622 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 5 OF 5 ************************* |--(resolution: 1.15 - 32.57 A, n_refl.=87577 (all), 4.91 % free)------------| | | | r_work= 0.1181 r_free= 0.1354 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.621775 | | target function (ml) not normalized (work): 301625.024073 | | target function (ml) not normalized (free): 15937.796032 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1190 0.1181 0.1354 n_refl.: 87577 re-set all scales: r(all,work,free)=0.1497 0.1495 0.1556 n_refl.: 87577 remove outliers: r(all,work,free)=0.1497 0.1495 0.1556 n_refl.: 87577 overall B=-0.01 to atoms: r(all,work,free)=0.1495 0.1493 0.1555 n_refl.: 87577 bulk-solvent and scaling: r(all,work,free)=0.1188 0.1180 0.1355 n_refl.: 87577 remove outliers: r(all,work,free)=0.1187 0.1179 0.1355 n_refl.: 87575 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 87.50 79 5 0.3963 286.346 248.929 0.441 1.000 0.314 11.894-9.307 95.10 93 4 0.2369 472.758 452.430 0.829 1.002 0.253 9.237-7.194 97.73 208 7 0.2459 384.554 378.846 0.919 1.002 0.170 7.162-5.571 100.00 427 22 0.2175 294.129 283.249 0.903 1.002 0.143 5.546-4.326 100.00 867 58 0.1140 403.767 399.246 0.953 1.002 0.140 4.315-3.360 100.00 1859 96 0.0952 383.985 381.477 0.994 1.002 0.140 3.356-2.611 100.00 3867 181 0.1154 252.258 250.125 0.999 1.002 0.110 2.608-2.026 99.99 8198 413 0.1020 167.224 166.447 1.013 1.001 0.000 2.025-1.573 100.00 17313 902 0.0963 81.664 81.923 1.027 1.000 0.000 1.573-1.221 100.00 36679 1900 0.1243 36.213 35.840 1.020 0.997 0.000 1.221-1.150 99.97 13689 708 0.2123 22.817 21.440 0.978 0.995 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0048 b_overall=-0.0237 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.1179 r_free=0.1355 After: r_work=0.1179 r_free=0.1354 ================================== NQH flips ================================== r_work=0.1179 r_free=0.1354 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 76 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 r_work=0.1179 r_free=0.1354 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1179 r_free=0.1354 | n_water=445 | time (s): 1.790 (total time: 1.790) Filter (dist) r_work=0.1179 r_free=0.1354 | n_water=445 | time (s): 35.910 (total time: 37.700) Filter (q & B) r_work=0.1180 r_free=0.1355 | n_water=443 | time (s): 3.050 (total time: 40.750) Compute maps r_work=0.1180 r_free=0.1355 | n_water=443 | time (s): 1.410 (total time: 42.160) Filter (map) r_work=0.1201 r_free=0.1372 | n_water=332 | time (s): 2.540 (total time: 44.700) Find peaks r_work=0.1201 r_free=0.1372 | n_water=332 | time (s): 0.460 (total time: 45.160) Add new water r_work=0.1258 r_free=0.1401 | n_water=489 | time (s): 2.900 (total time: 48.060) Refine new water occ: r_work=0.1193 r_free=0.1344 adp: r_work=0.1193 r_free=0.1347 occ: r_work=0.1180 r_free=0.1338 adp: r_work=0.1178 r_free=0.1340 occ: r_work=0.1170 r_free=0.1340 adp: r_work=0.1165 r_free=0.1339 ADP+occupancy (water only), MIN, final r_work=0.1165 r_free=0.1339 r_work=0.1165 r_free=0.1339 | n_water=489 | time (s): 231.870 (total time: 279.930) Filter (q & B) r_work=0.1172 r_free=0.1345 | n_water=455 | time (s): 3.710 (total time: 283.640) Filter (dist only) r_work=0.1172 r_free=0.1345 | n_water=455 | time (s): 36.580 (total time: 320.220) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 2.399794 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 47.941983 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1193 0.1370 0.0177 0.007 1.1 8.0 0.5 0.0 0 1.200 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.93 13.70 1.77 3.274 21.113 47.942 3.629 11.95 13.68 1.74 3.386 21.069 47.942 3.621 Individual atomic B min max mean iso aniso Overall: 9.23 102.31 21.16 2.04 222 1760 Protein: 9.23 102.31 16.70 2.04 0 1519 Water: 11.48 70.12 36.00 N/A 222 233 Other: 21.18 29.53 25.35 N/A 0 8 Chain A: 9.23 102.31 19.33 N/A 0 1760 Chain S: 15.65 70.12 35.68 N/A 222 0 Histogram: Values Number of atoms 9.23 - 18.54 1226 18.54 - 27.85 283 27.85 - 37.16 207 37.16 - 46.47 140 46.47 - 55.77 83 55.77 - 65.08 25 65.08 - 74.39 13 74.39 - 83.70 2 83.70 - 93.01 1 93.01 - 102.31 2 =========================== Idealize ADP of riding H ========================== r_work=0.1195 r_free=0.1368 r_work=0.1195 r_free=0.1368 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1195 r_free = 0.1368 target_work(ml) = 3.621 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1192 r_free = 0.1367 target_work(ml) = 3.621 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 1.15 - 32.57 A, n_refl.=87575 (all), 4.91 % free)------------| | | | r_work= 0.1192 r_free= 0.1367 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.620538 | | target function (ml) not normalized (work): 301514.814088 | | target function (ml) not normalized (free): 15949.022701 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 32.57 - 3.58 0.99 2917 171 0.1425 0.1417 5.6877 5.6446| | 2: 3.57 - 2.84 1.00 2888 124 0.1115 0.1439 5.1999 5.2726| | 3: 2.83 - 2.48 1.00 2820 163 0.1207 0.1253 5.0046 5.0216| | 4: 2.47 - 2.25 1.00 2825 136 0.1019 0.1150 4.7081 4.7615| | 5: 2.25 - 2.09 1.00 2756 127 0.0983 0.1120 4.6491 4.7421| | 6: 2.09 - 1.97 1.00 2846 113 0.0974 0.1225 4.3568 4.4689| | 7: 1.97 - 1.87 1.00 2787 165 0.0995 0.1251 4.0815 4.2024| | 8: 1.87 - 1.79 1.00 2789 144 0.1015 0.1240 3.9931 4.0795| | 9: 1.79 - 1.72 1.00 2745 138 0.0953 0.1294 3.7158 3.9213| | 10: 1.72 - 1.66 1.00 2831 160 0.0997 0.1219 3.631 3.7451| | 11: 1.66 - 1.61 1.00 2712 147 0.0964 0.1116 3.57 3.6159| | 12: 1.61 - 1.56 1.00 2773 144 0.0907 0.1150 3.3431 3.4841| | 13: 1.56 - 1.52 1.00 2745 130 0.0970 0.1048 3.3372 3.4389| | 14: 1.52 - 1.48 1.00 2803 134 0.0975 0.1120 3.2546 3.33| | 15: 1.48 - 1.45 1.00 2738 128 0.0999 0.1321 3.1637 3.3158| | 16: 1.45 - 1.42 1.00 2756 161 0.1059 0.1248 3.1437 3.2382| | 17: 1.42 - 1.39 1.00 2785 139 0.1111 0.1280 3.1105 3.2173| | 18: 1.39 - 1.36 1.00 2741 179 0.1136 0.1375 3.0799 3.2681| | 19: 1.36 - 1.34 1.00 2807 134 0.1201 0.1647 3.0871 3.292| | 20: 1.34 - 1.32 1.00 2696 147 0.1316 0.1488 3.0853 3.1452| | 21: 1.32 - 1.30 1.00 2785 112 0.1415 0.1627 3.0857 3.162| | 22: 1.29 - 1.27 1.00 2704 152 0.1466 0.1905 3.0836 3.2879| | 23: 1.27 - 1.26 1.00 2802 156 0.1564 0.1841 3.0993 3.2066| | 24: 1.26 - 1.24 1.00 2744 132 0.1623 0.1760 3.0939 3.1903| | 25: 1.24 - 1.22 1.00 2733 148 0.1791 0.2276 3.109 3.2852| | 26: 1.22 - 1.21 1.00 2727 135 0.1851 0.1789 3.1237 3.2035| | 27: 1.21 - 1.19 1.00 2814 148 0.1999 0.2126 3.1404 3.1539| | 28: 1.19 - 1.18 1.00 2671 147 0.2140 0.2325 3.14 3.1682| | 29: 1.18 - 1.16 1.00 2800 134 0.2217 0.2374 3.1274 3.2264| | 30: 1.16 - 1.15 1.00 2739 148 0.2373 0.2519 3.1172 3.1675| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |R-free likelihood based estimates for figures of merit, absolute phase error,| |and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)| | | | Bin Resolution No. Refl. FOM Phase Scale Alpha Beta | | # range work test error factor | | 1: 32.57 - 3.58 2917 171 0.95 9.14 1.00 0.97 6315.42| | 2: 3.57 - 2.84 2888 124 0.92 13.43 1.01 0.97 6315.42| | 3: 2.83 - 2.48 2820 163 0.89 17.60 0.99 0.97 5295.85| | 4: 2.47 - 2.25 2825 136 0.91 14.59 1.00 0.98 2666.71| | 5: 2.25 - 2.09 2756 127 0.89 16.90 1.01 0.98 2666.71| | 6: 2.09 - 1.97 2846 113 0.92 13.74 1.02 0.97 1570.09| | 7: 1.97 - 1.87 2787 165 0.94 10.96 1.02 0.97 634.83| | 8: 1.87 - 1.79 2789 144 0.91 14.50 1.00 0.97 634.83| | 9: 1.79 - 1.72 2745 138 0.93 11.46 0.98 0.97 342.09| | 10: 1.72 - 1.66 2831 160 0.93 12.32 0.98 0.97 283.46| | 11: 1.66 - 1.61 2712 147 0.93 12.89 0.98 0.97 270.49| | 12: 1.61 - 1.56 2773 144 0.95 9.58 0.99 0.97 148.15| | 13: 1.56 - 1.52 2745 130 0.94 11.15 1.02 0.97 148.15| | 14: 1.52 - 1.48 2803 134 0.94 11.30 1.02 0.97 132.16| | 15: 1.48 - 1.45 2738 128 0.95 10.35 1.01 0.98 102.88| | 16: 1.45 - 1.42 2756 161 0.94 11.57 1.02 0.98 102.88| | 17: 1.42 - 1.39 2785 139 0.94 11.40 1.01 0.98 93.09| | 18: 1.39 - 1.36 2741 179 0.94 11.72 1.01 0.98 87.43| | 19: 1.36 - 1.34 2807 134 0.94 12.24 1.00 0.98 87.43| | 20: 1.34 - 1.32 2696 147 0.94 12.44 0.99 0.97 82.65| | 21: 1.32 - 1.30 2785 112 0.94 13.35 0.98 0.96 82.31| | 22: 1.29 - 1.27 2704 152 0.93 13.91 0.98 0.96 82.46| | 23: 1.27 - 1.26 2802 156 0.92 14.81 0.98 0.95 83.20| | 24: 1.26 - 1.24 2744 132 0.92 14.97 0.97 0.95 83.20| | 25: 1.24 - 1.22 2733 148 0.91 16.39 0.96 0.94 84.84| | 26: 1.22 - 1.21 2727 135 0.90 18.12 1.02 0.93 86.66| | 27: 1.21 - 1.19 2814 148 0.89 18.77 1.02 0.93 86.66| | 28: 1.19 - 1.18 2671 147 0.88 20.36 1.01 0.92 90.36| | 29: 1.18 - 1.16 2800 134 0.88 20.67 0.99 0.92 91.75| | 30: 1.16 - 1.15 2739 148 0.86 22.10 0.98 0.92 91.75| |alpha: min = 0.92 max = 0.98 mean = 0.96| |beta: min = 82.31 max = 6315.42 mean = 985.33| |figures of merit: min = 0.00 max = 1.00 mean = 0.92| |phase err.(work): min = 0.00 max = 89.99 mean = 14.08| |phase err.(test): min = 0.00 max = 89.02 mean = 14.14| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.1201 0.1192 0.1367 n_refl.: 87575 re-set all scales: r(all,work,free)=0.1506 0.1504 0.1580 n_refl.: 87575 remove outliers: r(all,work,free)=0.1506 0.1504 0.1580 n_refl.: 87575 overall B=-0.01 to atoms: r(all,work,free)=0.1505 0.1503 0.1579 n_refl.: 87575 bulk-solvent and scaling: r(all,work,free)=0.1200 0.1192 0.1370 n_refl.: 87575 remove outliers: r(all,work,free)=0.1200 0.1191 0.1370 n_refl.: 87574 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 87.50 79 5 0.3989 286.346 250.267 0.447 0.998 0.314 11.894-9.307 94.12 92 4 0.2414 472.790 449.738 0.838 1.000 0.211 9.237-7.194 97.73 208 7 0.2483 384.554 377.952 0.915 1.000 0.120 7.162-5.571 100.00 427 22 0.2251 294.129 282.081 0.905 1.001 0.110 5.546-4.326 100.00 867 58 0.1205 403.767 398.752 0.963 1.001 0.110 4.315-3.360 100.00 1859 96 0.0994 383.985 381.489 1.005 1.001 0.108 3.356-2.611 100.00 3867 181 0.1175 252.258 250.251 1.010 1.001 0.100 2.608-2.026 99.99 8198 413 0.1033 167.224 166.338 1.024 1.001 0.000 2.025-1.573 100.00 17313 902 0.0975 81.664 81.936 1.035 1.001 0.000 1.573-1.221 100.00 36679 1900 0.1219 36.213 35.850 1.028 1.000 0.000 1.221-1.150 99.97 13689 708 0.2111 22.817 21.410 0.981 0.999 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0150 b_overall=-0.0171 ================= overall refinement statistics: step by step ================= ****************** REFINEMENT STATISTICS STEP BY STEP ****************** leading digit, like 1_, means number of macro-cycle 0 : statistics at the very beginning when nothing is done yet 1_bss: bulk solvent correction and/or (anisotropic) scaling 1_xyz: refinement of coordinates 1_adp: refinement of ADPs (Atomic Displacement Parameters) 1_wat: ordered solvent update (add / remove) 1_occ: refinement of occupancies ------------------------------------------------------------------------ stage r-work r-free bonds angles b_min b_max b_ave n_water shift 0 : 0.2606 0.1944 0.084 5.190 8.8 119.3 19.9 258 0.000 1_bss: 0.1636 0.1783 0.084 5.190 9.0 119.5 20.1 258 0.000 1_settarget: 0.1636 0.1783 0.084 5.190 9.0 119.5 20.1 258 0.000 1_nqh: 0.1636 0.1783 0.084 5.190 9.0 119.5 20.1 258 0.000 1_weight: 0.1636 0.1783 0.084 5.190 9.0 119.5 20.1 258 0.000 1_xyzrec: 0.1210 0.1465 0.008 0.968 9.0 119.5 20.1 258 0.118 1_adp: 0.1240 0.1541 0.008 0.968 8.6 118.8 21.0 258 0.118 1_regHadp: 0.1245 0.1546 0.008 0.968 8.6 118.8 21.0 258 0.118 1_occ: 0.1244 0.1547 0.008 0.968 8.6 118.8 21.0 258 0.118 2_bss: 0.1241 0.1538 0.008 0.968 8.7 118.9 21.1 258 0.118 2_settarget: 0.1241 0.1538 0.008 0.968 8.7 118.9 21.1 258 0.118 2_updatecdl: 0.1241 0.1538 0.008 0.977 8.7 118.9 21.1 258 0.118 2_nqh: 0.1242 0.1540 0.008 0.977 8.7 118.9 21.1 258 0.121 2_sol: 0.1232 0.1478 0.008 0.977 8.7 118.9 23.5 429 n/a 2_weight: 0.1232 0.1478 0.008 0.977 8.7 118.9 23.5 429 n/a 2_xyzrec: 0.1227 0.1505 0.007 0.878 8.7 118.9 23.5 429 n/a 2_adp: 0.1202 0.1473 0.007 0.878 8.8 113.9 23.2 429 n/a 2_regHadp: 0.1202 0.1472 0.007 0.878 8.8 113.9 23.2 429 n/a 2_occ: 0.1203 0.1468 0.007 0.878 8.8 113.9 23.2 429 n/a 3_bss: 0.1198 0.1466 0.007 0.878 8.8 114.0 23.2 429 n/a 3_settarget: 0.1198 0.1466 0.007 0.878 8.8 114.0 23.2 429 n/a 3_updatecdl: 0.1198 0.1466 0.007 0.879 8.8 114.0 23.2 429 n/a 3_nqh: 0.1198 0.1466 0.007 0.879 8.8 114.0 23.2 429 n/a 3_sol: 0.1226 0.1482 0.007 0.879 8.8 114.0 22.1 448 n/a 3_weight: 0.1226 0.1482 0.007 0.879 8.8 114.0 22.1 448 n/a 3_xyzrec: 0.1229 0.1453 0.006 0.918 8.8 114.0 22.1 448 n/a 3_adp: 0.1224 0.1417 0.006 0.918 9.2 109.6 21.8 448 n/a 3_regHadp: 0.1226 0.1418 0.006 0.918 9.2 109.6 21.8 448 n/a 3_occ: 0.1220 0.1417 0.006 0.918 9.2 109.6 21.8 448 n/a 4_bss: 0.1206 0.1379 0.006 0.918 9.2 109.5 21.8 448 n/a 4_settarget: 0.1206 0.1379 0.006 0.918 9.2 109.5 21.8 448 n/a 4_updatecdl: 0.1206 0.1379 0.006 0.917 9.2 109.5 21.8 448 n/a 4_nqh: 0.1206 0.1382 0.006 0.917 9.2 109.5 21.8 448 n/a 4_sol: 0.1202 0.1373 0.006 0.917 9.2 109.5 21.6 445 n/a 4_weight: 0.1202 0.1373 0.006 0.917 9.2 109.5 21.6 445 n/a 4_xyzrec: 0.1205 0.1371 0.006 0.941 9.2 109.5 21.6 445 n/a 4_adp: 0.1186 0.1357 0.006 0.941 9.2 106.0 21.3 445 n/a 4_regHadp: 0.1187 0.1357 0.006 0.941 9.2 106.0 21.3 445 n/a 4_occ: 0.1181 0.1354 0.006 0.941 9.2 106.0 21.3 445 n/a 5_bss: 0.1179 0.1355 0.006 0.941 9.2 106.0 21.2 445 n/a 5_settarget: 0.1179 0.1355 0.006 0.941 9.2 106.0 21.2 445 n/a 5_updatecdl: 0.1179 0.1355 0.006 0.942 9.2 106.0 21.2 445 n/a 5_setrh: 0.1179 0.1354 0.006 0.942 9.2 106.0 21.2 445 n/a 5_nqh: 0.1179 0.1354 0.006 0.942 9.2 106.0 21.2 445 n/a 5_sol: 0.1172 0.1345 0.006 0.942 9.2 106.0 21.2 455 n/a 5_weight: 0.1172 0.1345 0.006 0.942 9.2 106.0 21.2 455 n/a 5_xyzrec: 0.1193 0.1370 0.007 1.067 9.2 106.0 21.2 455 n/a 5_adp: 0.1195 0.1368 0.007 1.067 9.2 102.3 21.2 455 n/a 5_regHadp: 0.1195 0.1368 0.007 1.067 9.2 102.3 21.2 455 n/a 5_occ: 0.1192 0.1367 0.007 1.067 9.2 102.3 21.2 455 n/a end: 0.1191 0.1370 0.007 1.067 9.2 102.3 21.2 455 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_nowopt/shake_7718462_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_nowopt/shake_7718462_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 4.8000 Refinement macro-cycles (run) : 3696.5800 Write final files (write_after_run_outputs) : 56.5400 Total : 3757.9200 Total CPU time: 63.24 minutes =========================== phenix.refine: finished =========================== # Date 2024-12-28 Time 22:14:17 PST -0800 (1735452857.38 s) Start R-work = 0.1636, R-free = 0.1783 Final R-work = 0.1191, R-free = 0.1370 =============================================================================== Job complete usr+sys time: 3880.92 seconds wall clock time: 69 minutes 14.57 seconds (4154.57 seconds total)